Renaming VBCommunitySymbol.pm to VBCommunitySymbolParser.pm

misc-scripts/xref_mapping/XrefParser/VBCommunitySymbol.pm

-package XrefParser::VBCommunitySymbol;
- 
-use strict;
-use POSIX qw(strftime);
-use File::Basename;
- 
-use base qw( XrefParser::BaseParser );
-
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
-  if (scalar(@ARGV) != 1) {
-    print STDERR "\nUsage: VBCommunitySymbol.pm file <source_id> <species_id>\n\n";
-    exit(1);
-  }
-
-  run($ARGV[0]);
-
-}
-
-
-sub run {
-  my $self = shift if (defined(caller(1)));
-
-  my $source_id = shift;
-  my $species_id = shift;
-  my $files       = shift;
-  my $release_file   = shift;
-  my $verbose       = shift;
-
-  my $file = @{$files}[0];
-
-  print "source_id = $source_id, species= $species_id, file = $file\n" if($verbose);
-
-
-  if(!defined($source_id)){
-    $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
-  }
-  if(!defined($species_id)){
-    $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
-  }
-
-  my $added = 0;
-  my $count = 0;
-
-  my $file_io = $self->get_filehandle($file);
-
-  if ( !defined $file_io ) {
-    print STDERR "ERROR: Could not open file $file\n";
-    return 1;
-  }
-
-  while ( my $line = $file_io->getline() ) {
-    chomp $line;
-    my ($acc,$full_description, $gene_id)
-      = split("\t",$line);
-
-    my $xref_id = $self->get_xref($acc,$source_id, $species_id);
-    if(!defined($xref_id)){
-      $xref_id = $self->add_xref($acc,"", $acc, $full_description, $source_id, $species_id, "DIRECT");
-      $count++;
-    }
-    if(defined($gene_id) and $gene_id ne "-"){
-      $self->add_direct_xref($xref_id, $gene_id, "Gene", "") ;
-      $added++;
-    }	
-  }
-
-  $file_io->close();
-
-  print "Added $count xrefs and $added Direct xrefs to genes for VBCommunitySymbol\n" if($verbose);
-  return 0;
-}
-
-1;